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Sample GSM807199 Query DataSets for GSM807199
Status Public on Dec 08, 2011
Title B6 thymic NKT 2
Sample type RNA
 
Source name Sorted NKT cells replicate 2
Organism Mus musculus
Characteristics genetic background: C57BL/6
genotype: wt
source organ: thymus
cell type: NKT cells
Treatment protocol Single cell suspensions from 10 pooled thymi were enriched for T cells by MACS using PanT cell isolation kit (Miltenyi). NKT cells (CD3e+CD1d tetramer+) were then purified by flow sorting (FACSAria, Becton-Dickinson) from the enriched T cells.
Growth protocol Frest isolated NKT cells from indicated mouse strains
Extracted molecule total RNA
Extraction protocol RNA was isolated using a Qiagen Qiashredder followed by the Qiagen RNeasy kit according to the manufacturer's instructions. RNA yield was quantified spectrophotometrically (Nanodrop ND-1000) and aliquots electrophoresed to determine sample purity and concentration (Agilent 2100 Bioanalyzer).
Label Cy3
Label protocol standard Agilent protocol
 
Hybridization protocol Hybridizations were performed using One-colour hybridization on SurePrint G3 Mouse GE 60k Microarray (Agilent)
Scan protocol Slides were scanned using a GenePix 4000B Microarray scanner (Molecular Devices)
Description Gene expression of sorted thymic wildtype NKT cells
Data processing Images were processed with Agilent Feature Extraction software to generate raw probe intensity data, which was subsequently normalised by the quantile method. Differential expression analysis was carried out with an empirical Bayes approach on linear model using limma package.
 
Submission date Oct 03, 2011
Last update date Dec 08, 2011
Contact name Joyce Sebastian
E-mail(s) sebastian.joyce@vanderbilt.edu
Phone 615-322-1472
Organization name Vanderbilt University School of Medicine
Department Department of Microbiology and Immunology
Street address A-4223 Medical Centre North
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
 
Platform ID GPL13912
Series (1)
GSE32568 Gene expression comparison of wild-type and IL15ko thymic NKT cells

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
1 3177.061
2 15.561
3 17.561
4 17.561
5 24.561
6 17.561
7 17.561
8 22.561
9 113.561
10 22.561
11 27.561
12 17.561
13 97.561
14 1525.061
15 28.561
16 13.561
17 288.061
18 70.561
19 333.561
20 2998.561

Total number of rows: 62976

Table truncated, full table size 802 Kbytes.




Supplementary file Size Download File type/resource
GSM807199_B6_thymic_NKT_2.txt.gz 3.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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